Using two passports is also not appreciated in Malaysia, incidentally. It's on their computer too and they can spend time going through both passports and questioning your motives.
(9th August?) - actually, technically you did not. Your last stamp INTO the country from the land border is your arrival date (sometime in September). This matters if you do fill in the forms and apply for the extension.
It is fairly common for accommodation providers of all kinds to refuse to do a TM30, including some major hotels. But that explanation won't be accepted at Immigration, IF they ask for the TM30. It's possible that you'll need a Plan B.